R/windowedFit.R

In rbensua/afmToolkit: Functions for Atomic Force Microscope Force-Distance Curves Analysis

#' @title Linear fit in a running window
#' 
#' @description 
#' This is an internal function used by the \code{afmContactPoint} 
#' and \code{afmDetachPoint} functions. 
#' It computes the slopes of a linear fit to the data in a window of a given radius.
#' This function should not be used directly unless by experienced users.
#' @usage windowedFit(X, width)
#' @param X Least squares matrix on the form [1 z Force], 
#' according to input parameters in function \code{lm.fit} 
#' @param width Width of the window for the local regression (in vector position units)

#' @return \code{OUT} A vector of length \code{nrow(X)-2*width}, 
#' containing with the slopes of the fits.
#' @examples 
#' n <- 100
#' x <- seq(0,2*pi,length.out = n)
#' y = sin(x)+0.1*rnorm(n)
#' X <- matrix(c(rep(1,n),x,y),nrow = n,ncol = 3)
#' width <- 5
#' b <- windowedFit(X,width)
#' plot(x[(width+1):(n-width)],b,xlab = "x",ylab = "y",type = "l")
#' lines(x,y,col = "red")
#' legend("bottomleft",c("Slopes","Signal"),col = c(1,2),lty = 1)
#' @importFrom stats lm.fit
#' @export
windowedFit <- function(X, width){
  lenX <- dim(X)[1]
  SEQ1 <- seq(width+1,lenX-width)
  SEQ2 <- lapply(SEQ1, function(x) (x-width):(x+width))
  OUT <- lapply(SEQ2, function(a) coef(lm.fit(X[a,1:2],X[a,3]))[2])
  OUT <- simplify2array(OUT,higher=TRUE)
  return(OUT)
}